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WGLab / DeepMod2

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
MIT License
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Error！Deepmod2 analysis of human methylation #29

Open zzangcy opened 2 months ago

zzangcy commented 2 months ago

Hi, I encountered an error when I used the test BAM for analysis. It can't be resolved. I'm worried. Please help me. And our server does not have a GPU,The python version is v3.12,the code and error message are in the file. Thanks a lot, Freya

dm2-error.log

umahsn commented 2 months ago

Hi,

How did you basecall your FAST5 files? Can you share the exact command? DeepMod2 needs move table data either in BAM file or in the FAST5 file, depending upon how you basecall. It seems like your BAM file does not have move tables. If the move tables are in FAST5 file (only if you basecalled with Guppy v <6.4), use --fast5_move parameter.

If neither FAST5, nor the BAM file has move tables, you would need to rebasecall your reads using --moves_out parameter in Guppy, as shown here: https://github.com/WGLab/DeepMod2/blob/main/docs/Example.md#2-methylation-calling-from-fast5-files-with-guppy-basecalling. If you basecall with Guppy v>6.4, then the move table will be in BAM file and DeepMod2 will detect it and you wouldn't need to use --fast5_move parameter.

Umair

zzangcy commented 2 months ago

Hi,

How did you basecall your FAST5 files? Can you share the exact command? DeepMod2 needs move table data either in BAM file or in the FAST5 file, depending upon how you basecall. It seems like your BAM file does not have move tables. If the move tables are in FAST5 file (only if you basecalled with Guppy v <6.4), use --fast5_move parameter.

If neither FAST5, nor the BAM file has move tables, you would need to rebasecall your reads using --moves_out parameter in Guppy, as shown here: https://github.com/WGLab/DeepMod2/blob/main/docs/Example.md#2-methylation-calling-from-fast5-files-with-guppy-basecalling. If you basecall with Guppy v>6.4, then the move table will be in BAM file and DeepMod2 will detect it and you wouldn't need to use --fast5_move parameter.

Umair

Hi, Because the FAST5 files comes from a doctor who knows nothing about sequencing, I can't provide specific information about basecall, that's ok,I fully understand your explanation now👍, which is very important to me.Thanks so mush!🌼 Freya